I applied on 23rd Sep 2020 before FLR M decision and biometric done on 5th Nov 2020.I applied online with all supporting docs and cover letter explaining variation of visa .Actually the processing started now after biometric so just waiting for them to sort this for me.

Thank you all for your replies and help.
I am thinking to wait for ILR decision, may be they will themselves rectify their mistake.As one of you said Processing starts when biometric goes so hopefully they will now able to check into this.

Yes cover letter was sent online with all supporting documents.

Hi members ! Visa application FLR-M ( extension ) = 28th Jul 2020 Biometric in person = 22nd Sep 2020 Visa Granted = 6th Oct 2020 In the meanwhile I become eligible for ILR (10 year route) Visa application for ILR = 23 Sep 2020 My questions is that why home office did not acknowledge the ILR ...